PhenomizerToNetwork

PhenomizerToNetwork generates and displays a disease network for the diseases of PhenoDis. The aim of the node is to visualize the predictions of Phenomizer within this network.
The node requires the program Cytoscape (recommended version 3.2.1) to show the resulting network.

The input of PhenomizerToNetwork consists of two different tables. The first table is the output of Phenomizer (including disease_ids and scores). The second table is a symmetric all-against-all matrix containing distance or similarity values for pairs of diseases. All columns have to be named with PhenoDis disease_ids except for one optional column with disease names. Furthermore, the row ids of the table have to be PhenoDis disease_ids. An example for such a matrix table is provided at https://github.com/marie-sophie/mapra.

The node does not produce any output table, but writes 4 files into a specified output directory.

• disease_network.xgmml: an xml-based representation of the disease network
• script.txt: a script using the Cytoscape scripting language
• cytoscape_out.txt: everything that Cytoscape writes to stdout
• cytoscape_err.txt: everything that Cytoscape writes to stderr (usually empty)

Options

Comparator

The comparator defines a rule for generating the edges of the disease network.
If the matrix at input port 1 is a distance matrix, use <. If the matrix at input port 1 is a similarity matrix, use >.

Edge threshold

The option refers to the scores stored in the matrix at input port 1. If an entry of the table fulfills the threshold, PhenomizerToNetwork creates an edge between the corresponding diseases.

Output directory

PhenomizerToNetwork generates several text-based files. All these files are written to the specified directory.

Run Cytoscape

The Run Cytoscape option allows starting Cytoscape during the execution of the node. Alternatively, you can run Cytoscape manually using the command:
cytoscape.sh -S script.txt

Cytoscape executable

The file chooser is active only if the Run Cytoscape option is ticked. The option requires a script called cytoscape.sh (part of the Cytoscape installation).

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